The first time she set the 800 metres record was in late June 2012 while narrowly winning the 2012 African Championships in Athletics in 1:59.11 in what was only her third competitive race.

Two days later, she finished seventh (subsequently upgraded to fifth as a result of the doping disqualifications of Russian athletes Elena Arzhakova and Mariya Savinova) in the final.

In 2017, Niyonsaba earned a new personal best and national record at the Monaco Diamond League after winning the 800 m there in a time of 1:55.47 on July 21.

She led throughout the majority of the race, but Caster Semenya used her phenomenal final kick to pass the Burundian on the home stretch once again and win gold.

In 2019, it was revealed that Niyonsaba was born with the 46,XY karyotype and an intersex condition after her qualification for IAAF women's competition was affected[how?]

by the association's new regulations for athletes with XY differences of sexual development, testosterone levels above 5 nmol/L, and androgen sensitivity.